Archive for the ‘Development’ Category
Monday, April 20th, 2009
We are pleased to announce Biopython release 1.50, featuring some significant additions since Biopython 1.49 was released late last year.
GenomeDiagram by Leighton Pritchard has been integrated into Biopython as the Bio.Graphics.GenomeDiagram module.
A new module Bio.Motif has been added, which is intended to replace the existing Bio.AlignAce and Bio.MEME modules. Also ...
Posted in Biopython, Community, Development, OBF, OBF Projects | 2 Comments »
Friday, April 3rd, 2009
We are pleased to announce a beta release of Biopython 1.50 for public testing. There have been some significant changes since Biopython 1.49 was released late last year.
GenomeDiagram by Leighton Pritchard has been integrated into Biopython as the Bio.Graphics.GenomeDiagram module.
A new module Bio.Motif has been added, which is intended to ...
Posted in Biopython, Community, Development, OBF Projects | No Comments »
Thursday, March 26th, 2009
Those of you doing next generation sequencing may be pleased to know that the next release of Biopython is expected to include support for reading and writing FASTQ and QUAL files within our Bio.SeqIO interface. These formats are used for traditional Sanger capillary sequencing, and Roche 454 sequencing (Roche ...
Posted in Biopython, Code, Development, OBF | Comments Off
Tuesday, March 17th, 2009
Initially for evaluation purposes only, Giovanni and Bartek have setup a mirror of Biopython on GitHub, which is automatically updated from the OBF hosted Biopython CVS repository. See our git migration wiki page for details. If this is favorably received, then moving Biopython from CVS to git seems ...
Posted in Biopython, Code, Community, Development, OBF | 1 Comment »
Tuesday, March 10th, 2009
A wiki page for collecting ideas, possible projects, prerequisites, possible solution approaches, mentors, other people or channels to contact for more information or to bounce ideas off of, etc. has been setup:
http://open-bio.org/wiki/Google_Summer_Code_2009
Posted in Code, Community, Development, Documentation, General, OBF, OBF Projects | No Comments »
Thursday, February 26th, 2009
All,
I am proud to announce that the 1.6 release for BioPerl-run, BioPerl-
db, and BioPerl-network are now available by direct download and via
CPAN. These are designated as 1.006000, with a requirement for
BioPerl 1.6 and higher (1.006000).
FIXED:
1) Bio::Tools::Run::Primer3 now accepts primer3 or primer3_core as
executable ...
Posted in BioPerl, Code, Development, Documentation | No Comments »
Wednesday, February 25th, 2009
Hi all,
We are pleased to announce the release of BioRuby 1.3.0.
The archive is available at:
http://bioruby.org/archive/bioruby-1.3.0.tar.gz
Web page:
http://bioruby.org/
http://bioruby.open-bio.org/
API documentation:
http://bioruby.org/rdoc/
Bug report:
http://rubyforge.org/projects/bioruby/
(Updating of http://bioruby.rubyforge.org/ is still
in progress. Please wait for a moment.)
We also put RubyGems pacakge at RubyForge as always.
You can easily install by ...
Posted in BioRuby, Code, Development, Documentation | No Comments »
Tuesday, February 24th, 2009
Please forward as appropriate and forgive multiple postings.
Call for Abstracts for the 2009 Bioinformatics Open Source Conference (BOSC) 2009
An ISMB 2009 Special Interest Group (SIG)
Date: June 27-28, 2009
Location: Stockholm, Sweden
URL: http://www.open-bio.org/wiki/BOSC_2009
Abstract submission via EasyChair:
https://www.easychair.org/login.cgi?conf=bosc2009
Important Dates
Monday, April 13: Abstract deadline
May 1, 2009: Notification of accepted abstracts
May 15, 2009: Early Registration ...
Posted in BOSC/ISMB, Code, Community, Development, General, OBF, OBF Projects | No Comments »
Friday, February 13th, 2009
Google is committed to run the Summer of Code program again this year. It will be for the 5th time.
In broad strokes, the program funds what you might call remote summer internships for students to contribute to an open-source software project. Projects (or umbrella organizations) wishing to participate in the program ...
Posted in Code, Community, Development, General, OBF, OBF Projects | No Comments »
Sunday, January 25th, 2009
Release Pumpkin Chris Fields has announced the release of BioPerl 1.6 - the first stable release in a several years containing many significant improvements and bug fixes.
I am proud to announce, on behalf of the BioPerl core developers, that BioPerl 1.6.0 is now available. This is the first BioPerl core ...
Posted in BioPerl, Code, Development | No Comments »